[Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?

[luke at stat.uiowa.edu]

On Mon, 12 Apr 2010, William Dunlap wrote:

>
>> -----Original Message-----
>> From: r-devel-bounces at r-project.org
>> [mailto:r-devel-bounces at r-project.org] On Behalf Of Henrik Bengtsson
>> Sent: Monday, April 12, 2010 8:24 AM
>> To: Duncan Murdoch
>> Cc: r-devel; Michael Dewey
>> Subject: Re: [Rd] R CMD check tells me 'no visible binding
>> for globalvariable ', what does it mean?
>>
>> On Mon, Apr 12, 2010 at 5:08 PM, Duncan Murdoch
>> <murdoch at stats.uwo.ca> wrote:
>>> On 12/04/2010 10:51 AM, Michael Dewey wrote:
>>>>
>>>> When I run R CMD check on a package I have recently
>> started work on I get
>>>> the following:
>>>>
>>>> * checking R code for possible problems ... NOTE
>>>> addlinear: no visible binding for global variable 'x'
>>>>
>>>> I appreciate that this is only a NOTE and so I assume is
>> R's equivalent of
>>>> 'This is perfectly legal but I wonder whether it is really what you
>>>> intended' but I would like to understand it.
>>>>
>>>> In the relevant function addlinear the following function
>> is defined
>>>> locally:
>>>>
>>>>    orfun <- function(x, oddsratio) {1/(1+1/(oddsratio *
>> (x/(1-x))))}
>>>>
>>>> and then used later in curve
>>>>
>>>>       curve(orfun(x, exp(estimate)), from = 0.001, to =
>> 0.999, add = TRUE)
>>>>
>>>> These are the only occurrences of 'x'.
>>>>
>>>> Is it just telling me that I have never assigned a value
>> to x? Or is it
>>>> more sinister than that? As far as I can tell the function
>> does what I
>>>> intended.
>>>
>>> The curve() function evaluates the first argument in a
>> strange way, and this
>>> confuses the code checking.  (The variable name "x" is
>> special to curve().)
>>>
>>> I think you can avoid the warning by rewriting that call to
>> curve() as
>>>
>>> curve(function(x) orfun(x, exp(estimate)), from = 0.001, to
>> = 0.999, add =
>>> TRUE)
>>
>> ...or
>>
>> x <- NULL; rm(x); # Dummy to trick R CMD check
>> curve(orfun(x, exp(estimate)), from = 0.001, to = 0.999, add = TRUE)
>
> Or we could come up with a scheme to telling the usage checking functions
> in codetools that some some or all arguments of certain functions
> are evaluated in odd ways so it should not check them.  E.g.,
>   irregularUsage(curve, expr)
>   irregularUsage(lm, subset, formula) # subset and formula arguments of lm
>   irregularUsage(expression, ...) # ... arguments to expression
> Perhaps one could add such indications to the NAMESPACE file
> or to a new file in a package.  The former is kludgy but the
> latter requires changes to the packaging system.
>

This is done at the moment in a very ad hoc way for functions in the
core packages.  I will make a note to add something for curve.  This
is an interesting case, as only the variable 'x' should be viewed as
special for code analysis purposes if I understand the intent in curve
properly.

Providing a mechanism for user functions to be annotated for code
analysis might be useful, and might help in making the handling of
core package functions with special evaluation rulesa little less ad
hloc.  On the other hand I'm not sure I want to do anything that
encourages further use of nonstantard evaluation in new code.

luke

> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
>
>>
>> /Henrik
>>
>>>
>>> Duncan Murdoch
>>>
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>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
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>>
>
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-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu